Project name: Reddy2_Project_002
Run name: 230411_VH00601_152_AACLJHTM5
Read type: Single-end 101bp
Samples: 138
Total reads: 340,640,215
Mean reads per sample: 2,468,407
Report generated: Wed Apr 12 10:47:53 CDT 2023

Instrument: nextseq P2

More details
Fastq folder: /spaces/umgc/illumina_analysis/230411_VH00601_152_AACLJHTM5-analysis/demultiplex_20230412-10-45-36/demultiplex/Reddy2_Project_002
Commandline: /panfs/jay/groups/21/umgc/public/bin/gopher-pipelines/2.3/bin/illumina-pipeline.pl –fastqfolder /spaces/umgc/illumina_analysis/230411_VH00601_152_AACLJHTM5-analysis/demultiplex_20230412-10-45-36/demultiplex/Reddy2_Project_002 –samplespernode 20 –threadspersample 6 –projectname Reddy2_Project_002 –runname 230411_VH00601_152_AACLJHTM5 –illuminasamplesheet /spaces/umgc/illumina_analysis/230411_VH00601_152_AACLJHTM5-analysis/demultiplex_20230412-10-45-36/SampleSheet.csv –threads 20 –scratchfolder /spaces/umgc/tmp/scratch/230411_VH00601_152_AACLJHTM5/demultiplex_20230412-10-45-36/Reddy2_Project_002/illumina-basicQC
Gopher-pipelines version: 2.3
Program versions
/panfs/roc/soft/modulefiles.legacy/modulefiles.common/java/jdk1.7.0_45
R/3.5.0
advisor/2018/release
bowtie2/2.3.4.1.CentOS7
bzip2/1.0.6-gnu6.1.0_PIC
bzip2/1.0.6-gnu7.2.0_PIC
curl/7.59.0_gcc7.2.0
ensembl/1.0
fastqc/0.11.7
gcc/7.2.0
gcc/8.1.0
genomes-other/1.0
genomes/1.0
gmp/6.1.2_gcc7.2.0
gmp/6.1.2_gcc8.1.0
gopher-pipelines/2.3
gtools/2.3
impi/2018/release_singlethread
inspector/2018/release
intel/2018/release
intel/cluster/2018
isl/0.18_gcc7.2.0
isl/0.19_gcc8.1.0
itac/2018/release
libtiff/4.0.8
mpc/1.0.3_gcc7.2.0
mpc/1.1.0_gcc8.1.0
mpfr/3.1.6_gcc7.2.0
mpfr/4.0.1_gcc8.1.0
pandoc/2.3
parallel/20210822
pcre/8.42_gcc7.2.0
perlmodules/1.0
plotly/20190228
pysam/0.15.3
python2/2.7.15_anaconda
python3/3.8.3_anaconda2020.07_mamba
samtools/1.9
texlive/20131202
trimmomatic/0.33
umgc/1.0
vtune/2018/release
xz-utils/5.2.3_gcc7.2.0
zlib/1.2.11_gcc7.2.0
zlib/1.2.8
Metric table
general.projectname general.readlength general.runname subsample.rawreads subsample.subsampledreads fastqc.meanreadqualityR1 fastqc.pct.adapter fastqc.pct.deduplicated fastqc.pct.dimer fastqc.pct.gc fastqc.sequencelength fastqc.totalsequences fastqspeciesscreen.pct.Adapters fastqspeciesscreen.pct.Chloroplast fastqspeciesscreen.pct.Mitochondria fastqspeciesscreen.pct.NoHit fastqspeciesscreen.pct.PhiX fastqspeciesscreen.pct.Vectors fastqspeciesscreen.pct.ecoli fastqspeciesscreen.pct.human fastqspeciesscreen.pct.mouse fastqspeciesscreen.pct.rRNA
106.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2506344 2506344 31.90 5.89 63.97 0.09 57.00 101 2000000 0.00 0.00 0 94.13 0.00 0.00 0.00 0.14 0.46 5.27
107.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 189950 189950 28.80 4.28 40.28 3.22 65.00 101 189950 0.00 0.00 0 72.00 0.00 0.00 0.04 1.81 17.01 9.14
108.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2591004 2591004 31.90 5.84 63.69 0.13 57.00 101 2000000 0.00 0.00 0 94.00 0.00 0.00 0.00 0.21 0.55 5.24
109.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2594739 2594739 31.90 5.31 64.32 0.07 56.00 101 2000000 0.00 0.00 0 95.05 0.00 0.00 0.00 0.57 0.16 4.22
110.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2868088 2868088 31.80 6.35 62.94 0.10 57.00 101 2000000 0.00 0.00 0 93.37 0.00 0.00 0.00 0.15 0.60 5.88
111.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3375231 3375231 31.80 6.69 63.17 0.10 57.00 101 2000000 0.00 0.00 0 93.13 0.00 0.00 0.00 0.59 0.27 6.01
112.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2609344 2609344 31.80 5.48 64.58 0.08 56.00 101 2000000 0.00 0.00 0 94.08 0.00 0.00 0.00 0.14 0.65 5.13
113.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2627003 2627003 31.80 5.13 65.58 0.11 56.00 101 2000000 0.00 0.00 0 94.56 0.00 0.00 0.00 0.66 0.18 4.60
114.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2724451 2724451 31.90 2.82 67.35 0.03 55.00 101 2000000 0.00 0.00 0 96.92 0.00 0.00 0.00 0.55 0.15 2.38
115.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1898602 1898602 31.90 2.10 69.25 0.03 54.00 101 1898602 0.00 0.00 0 97.43 0.00 0.00 0.00 0.20 0.60 1.77
116.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2422434 2422434 31.90 2.82 67.69 0.04 55.00 101 2000000 0.00 0.00 0 96.51 0.00 0.00 0.00 0.19 0.70 2.60
117.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2327138 2327138 31.90 2.10 68.26 0.03 54.00 101 2000000 0.00 0.00 0 97.54 0.00 0.00 0.00 0.20 0.64 1.62
118.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1259286 1259286 30.80 1.54 81.26 0.01 54.00 101 1259286 0.00 0.00 0 97.62 0.00 0.00 0.00 0.72 0.27 1.39
119.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1369767 1369767 31.70 2.35 76.87 0.02 54.00 101 1369767 0.00 0.00 0 97.29 0.00 0.00 0.00 0.60 0.13 1.98
120.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2120657 2120657 31.50 2.50 70.22 0.03 55.00 101 2000000 0.00 0.00 0 97.49 0.00 0.00 0.00 0.11 0.68 1.72
121.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2667719 2667719 31.90 2.35 67.47 0.03 54.00 101 2000000 0.00 0.00 0 97.48 0.00 0.00 0.00 0.22 0.76 1.54
122.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3185571 3185571 31.90 5.59 64.47 0.11 56.00 101 2000000 0.00 0.00 0 93.71 0.00 0.00 0.00 0.74 0.28 5.27
123.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3582230 3582230 31.90 5.82 64.11 0.12 57.00 101 2000000 0.00 0.00 0 93.43 0.00 0.00 0.00 0.50 0.18 5.89
124.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3272026 3272026 31.90 6.15 63.58 0.14 57.00 101 2000000 0.00 0.00 0 93.15 0.00 0.00 0.00 0.58 0.23 6.04
125.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2724753 2724753 31.90 4.78 65.86 0.13 56.00 101 2000000 0.00 0.00 0 94.26 0.00 0.00 0.00 0.86 0.29 4.59
126.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3285465 3285465 31.90 5.96 64.12 0.11 57.00 101 2000000 0.01 0.00 0 93.65 0.00 0.00 0.00 0.62 0.15 5.57
127.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3332286 3332286 31.90 7.08 63.83 0.16 57.00 101 2000000 0.01 0.00 0 92.48 0.00 0.00 0.00 0.24 0.51 6.76
128.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3234405 3234405 31.90 5.93 62.64 0.10 57.00 101 2000000 0.00 0.00 0 93.12 0.00 0.00 0.00 0.55 0.23 6.10
129.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3177782 3177782 31.90 6.11 64.95 0.14 56.00 101 2000000 0.00 0.00 0 92.90 0.00 0.00 0.00 0.17 0.66 6.27
130.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3276248 3276248 31.80 5.29 63.99 0.07 56.00 101 2000000 0.00 0.00 0 94.51 0.00 0.00 0.00 0.60 0.19 4.70
131.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2935832 2935832 31.90 4.70 63.62 0.07 56.00 101 2000000 0.00 0.00 0 94.82 0.00 0.00 0.00 0.17 0.66 4.35
132.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2779558 2779558 31.90 4.22 64.51 0.05 56.00 101 2000000 0.00 0.00 0 95.98 0.00 0.00 0.00 0.61 0.22 3.19
133.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2846721 2846721 31.90 4.72 65.16 0.08 56.00 101 2000000 0.00 0.00 0 95.27 0.00 0.00 0.00 0.60 0.24 3.89
134.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2769614 2769614 31.40 4.93 68.01 0.07 56.00 101 2000000 0.00 0.00 0 94.92 0.00 0.00 0.00 0.61 0.16 4.31
135.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2941781 2941781 31.50 5.34 66.92 0.08 57.00 101 2000000 0.00 0.00 0 94.09 0.00 0.00 0.00 0.28 0.74 4.89
136.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2679271 2679271 31.80 4.94 64.49 0.06 56.00 101 2000000 0.00 0.00 0 95.18 0.00 0.00 0.00 0.18 0.43 4.21
137.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2424832 2424832 31.60 1.74 66.78 0.36 53.00 101 2000000 0.00 0.00 0 95.71 0.00 0.00 0.00 0.41 1.53 2.35
138.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2564195 2564195 31.70 4.07 66.11 0.39 56.00 101 2000000 0.00 0.00 0 94.79 0.00 0.00 0.00 0.37 1.02 3.82
139.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2684855 2684855 31.80 4.86 64.61 0.08 56.00 101 2000000 0.00 0.00 0 94.83 0.00 0.00 0.00 0.63 0.22 4.32
140.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2380192 2380192 31.60 3.73 65.73 0.45 57.00 101 2000000 0.00 0.00 0 94.35 0.00 0.00 0.00 1.40 0.71 3.54
141.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1953793 1953793 31.50 1.26 64.10 0.42 55.00 101 1953793 0.00 0.00 0 94.91 0.00 0.00 0.00 3.17 1.01 0.91
142.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2531600 2531600 31.60 3.86 64.33 0.30 54.00 101 2000000 0.00 0.00 0 95.00 0.00 0.00 0.00 0.30 0.91 3.79
143.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2475733 2475733 31.30 1.96 60.87 0.61 55.00 101 2000000 0.00 0.00 0 94.85 0.00 0.00 0.01 0.91 2.97 1.26
144.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2236239 2236239 31.60 3.01 64.27 0.25 54.00 101 2000000 0.00 0.00 0 95.55 0.00 0.00 0.00 0.32 1.18 2.95
145.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2721950 2721950 31.80 4.98 64.92 0.14 56.00 101 2000000 0.00 0.00 0 94.60 0.00 0.00 0.00 0.73 0.22 4.45
146.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1706525 1706525 31.60 1.35 48.46 0.41 54.00 101 1706525 0.00 0.00 0 95.22 0.00 0.00 0.00 2.81 0.76 1.21
147.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3145679 3145679 31.90 4.63 65.80 0.10 56.00 101 2000000 0.00 0.00 0 94.79 0.00 0.00 0.00 0.28 0.76 4.17
148.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3016728 3016728 31.80 4.19 66.21 0.25 55.00 101 2000000 0.00 0.01 0 94.25 0.00 0.00 0.01 0.41 1.06 4.26
149.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2793641 2793641 31.80 3.46 66.53 0.17 56.00 101 2000000 0.00 0.00 0 95.76 0.00 0.00 0.00 0.29 1.01 2.94
150.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2852724 2852724 31.70 2.21 59.19 0.30 51.00 101 2000000 0.00 0.00 0 96.52 0.00 0.00 0.00 0.24 1.00 2.24
151.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3400637 3400637 31.60 5.00 67.51 0.08 57.00 101 2000000 0.00 0.00 0 94.41 0.00 0.00 0.00 0.66 0.22 4.71
152.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2967980 2967980 31.80 4.56 63.95 0.08 57.00 101 2000000 0.00 0.00 0 95.10 0.00 0.00 0.00 0.21 0.57 4.12
153.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3114740 3114740 31.90 5.26 64.81 0.10 57.00 101 2000000 0.00 0.00 0 94.13 0.00 0.00 0.00 0.24 0.67 4.96
154.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2948404 2948404 31.80 4.05 63.27 0.18 56.00 101 2000000 0.00 0.00 0 94.88 0.00 0.00 0.00 0.37 0.91 3.84
155.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2531445 2531445 31.70 2.16 61.70 0.38 52.00 101 2000000 0.00 0.00 0 95.62 0.00 0.00 0.00 0.36 1.54 2.48
156.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3019200 3019200 31.90 4.30 65.38 0.14 56.00 101 2000000 0.00 0.00 0 94.73 0.00 0.00 0.00 0.23 0.83 4.21
157.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2887290 2887290 31.90 4.07 64.83 0.13 56.00 101 2000000 0.00 0.00 0 94.93 0.00 0.00 0.00 0.28 0.81 3.98
158.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3076741 3076741 31.70 4.16 67.28 0.10 56.00 101 2000000 0.00 0.00 0 95.56 0.00 0.00 0.00 0.61 0.30 3.53
159.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3096768 3096768 31.80 4.69 64.40 0.07 56.00 101 2000000 0.00 0.00 0 94.87 0.00 0.00 0.00 0.48 0.18 4.47
16.2nd.seq.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2768707 2768707 31.70 4.47 65.11 0.12 56.00 101 2000000 0.00 0.00 0 94.69 0.00 0.00 0.00 0.20 0.73 4.38
160.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3040254 3040254 31.70 4.03 65.08 0.14 56.00 101 2000000 0.00 0.00 0 95.12 0.00 0.00 0.00 0.32 0.86 3.70
161.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3237602 3237602 31.80 4.34 64.91 0.11 56.00 101 2000000 0.00 0.00 0 95.26 0.00 0.00 0.00 0.24 0.65 3.85
162.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3433327 3433327 31.90 4.81 63.74 0.05 56.00 101 2000000 0.00 0.00 0 94.86 0.00 0.00 0.00 0.48 0.22 4.44
163.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2909579 2909579 31.90 3.81 66.20 0.12 56.00 101 2000000 0.00 0.00 0 95.46 0.00 0.00 0.00 0.24 0.72 3.58
164.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2887200 2887200 31.80 4.43 65.70 0.20 56.00 101 2000000 0.00 0.00 0 94.38 0.00 0.00 0.00 0.40 0.92 4.30
165.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2827721 2827721 31.90 4.38 65.87 0.11 56.00 101 2000000 0.00 0.00 0 94.76 0.00 0.00 0.00 0.23 0.70 4.31
166.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3208668 3208668 31.80 4.91 64.84 0.07 57.00 101 2000000 0.00 0.00 0 94.23 0.00 0.00 0.00 0.70 0.21 4.86
167.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3554467 3554467 31.80 4.78 65.83 0.12 56.00 101 2000000 0.00 0.00 0 94.37 0.00 0.00 0.00 0.22 0.76 4.65
168.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2854677 2854677 31.60 4.17 66.03 0.16 56.00 101 2000000 0.01 0.00 0 94.75 0.00 0.00 0.00 0.30 0.77 4.17
169.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3017118 3017118 31.90 4.57 65.58 0.08 56.00 101 2000000 0.00 0.00 0 95.03 0.00 0.00 0.00 0.20 0.55 4.22
170.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3032701 3032701 31.90 4.36 61.67 0.01 56.00 101 2000000 0.00 0.00 0 96.04 0.00 0.00 0.00 0.50 0.13 3.33
171.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2807443 2807443 32.00 5.33 60.95 0.01 57.00 101 2000000 0.00 0.00 0 94.95 0.00 0.00 0.00 0.42 0.14 4.49
172.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2935637 2935637 32.00 4.11 62.67 0.01 56.00 101 2000000 0.00 0.00 0 96.18 0.00 0.00 0.00 0.51 0.14 3.17
173.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2901769 2901769 32.00 4.10 62.19 0.01 56.00 101 2000000 0.00 0.00 0 96.52 0.00 0.00 0.00 0.45 0.11 2.92
174.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3061495 3061495 31.90 3.84 61.89 0.01 56.00 101 2000000 0.00 0.00 0 96.18 0.00 0.00 0.00 0.48 0.11 3.23
175.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3407818 3407818 31.90 5.12 61.56 0.01 58.00 101 2000000 0.00 0.00 0 95.00 0.00 0.00 0.00 0.63 0.24 4.13
176.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2670367 2670367 31.90 3.86 62.10 0.01 56.00 101 2000000 0.00 0.00 0 96.82 0.00 0.00 0.00 0.43 0.11 2.64
177.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2777903 2777903 32.00 3.70 62.88 0.01 56.00 101 2000000 0.00 0.01 0 96.62 0.00 0.00 0.00 0.17 0.49 2.71
178.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2320718 2320718 31.90 4.25 62.02 0.03 56.00 101 2000000 0.00 0.00 0 95.74 0.00 0.00 0.00 0.49 0.19 3.58
179.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2803861 2803861 31.90 5.35 62.97 0.04 56.00 101 2000000 0.00 0.00 0 94.96 0.00 0.00 0.00 0.42 0.09 4.53
180.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2236486 2236486 32.00 2.76 62.56 0.01 56.00 101 2000000 0.00 0.00 0 97.37 0.00 0.00 0.00 0.57 0.19 1.87
181.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2433663 2433663 31.90 4.46 62.83 0.02 57.00 101 2000000 0.00 0.00 0 94.87 0.00 0.00 0.46 0.55 0.18 3.94
182.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3137589 3137589 31.90 4.26 63.24 0.01 56.00 101 2000000 0.00 0.00 0 96.07 0.00 0.00 0.00 0.48 0.13 3.32
183.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2829924 2829924 31.90 3.32 64.17 0.01 56.00 101 2000000 0.00 0.00 0 96.97 0.00 0.00 0.00 0.53 0.21 2.29
184.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2107661 2107661 31.90 3.14 64.14 0.00 55.00 101 2000000 0.00 0.00 0 97.08 0.00 0.00 0.00 0.52 0.12 2.28
185.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2500541 2500541 31.90 3.49 63.37 0.01 56.00 101 2000000 0.00 0.00 0 97.28 0.00 0.00 0.00 0.44 0.11 2.17
186.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2884575 2884575 31.80 7.24 62.14 0.20 58.00 101 2000000 0.00 0.00 0 92.06 0.01 0.00 0.42 0.14 0.40 6.97
187.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 140161 140161 29.80 3.44 60.26 1.91 63.00 101 140161 0.00 0.00 0 84.19 0.00 0.02 0.40 1.36 11.14 2.89
188.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1904604 1904604 31.80 2.68 28.93 0.21 55.00 101 1904604 0.00 0.00 0 94.18 0.00 0.00 3.26 0.06 0.54 1.96
189.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2821040 2821040 31.90 8.93 29.26 0.04 61.00 101 2000000 0.00 0.00 0 90.78 0.00 0.01 0.42 0.01 0.07 8.71
190.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2609991 2609991 31.90 5.18 44.10 0.07 58.00 101 2000000 0.00 0.00 0 95.23 0.00 0.00 0.05 0.26 0.10 4.36
191.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2522207 2522207 31.70 6.27 63.66 0.35 59.00 101 2000000 0.00 0.00 0 92.81 0.00 0.00 0.00 0.25 0.89 6.05
192.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2127564 2127564 31.70 6.29 63.13 0.48 59.00 101 2000000 0.00 0.00 0 92.27 0.00 0.00 0.00 0.25 1.12 6.36
193.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2208139 2208139 31.70 7.57 57.77 0.51 61.00 101 2000000 0.00 0.00 0 91.06 0.00 0.00 0.00 0.27 0.93 7.74
194.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 591156 591156 31.80 5.11 77.16 0.21 60.00 101 591156 0.00 0.00 0 94.30 0.00 0.00 0.00 0.30 0.78 4.62
195.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 509094 509094 31.90 2.85 80.11 0.14 58.00 101 509094 0.00 0.00 0 96.39 0.00 0.00 0.00 0.87 0.25 2.49
196.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 838350 838350 32.00 2.94 77.41 0.06 58.00 101 838350 0.00 0.00 0 96.63 0.00 0.00 0.00 0.63 0.24 2.50
197.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 336950 336950 31.70 3.93 82.72 0.17 59.00 101 336950 0.00 0.00 0 94.72 0.00 0.00 0.01 0.35 0.83 4.09
198.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1567372 1567372 32.00 2.64 69.74 0.03 57.00 101 1567372 0.00 0.00 0 97.11 0.00 0.00 0.00 0.45 0.19 2.25
199.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2481945 2481945 31.90 3.50 63.40 0.05 58.00 101 2000000 0.00 0.00 0 96.54 0.00 0.00 0.00 0.20 0.51 2.75
200.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2188477 2188477 31.90 3.75 59.32 0.06 60.00 101 2000000 0.00 0.00 0 95.78 0.00 0.00 0.00 0.21 0.65 3.36
201.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 391852 391852 31.90 4.23 81.50 0.19 59.00 101 391852 0.00 0.00 0 95.06 0.00 0.00 0.00 0.30 0.91 3.73
202.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3288143 3288143 31.90 8.18 61.55 0.17 59.00 101 2000000 0.00 0.00 0 91.08 0.00 0.00 0.00 0.51 0.11 8.30
203.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3606740 3606740 31.90 7.79 60.33 0.27 59.00 101 2000000 0.00 0.00 0 90.99 0.00 0.00 0.00 0.52 0.25 8.24
205.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2024268 2024268 31.80 1.71 65.98 0.41 54.00 101 2000000 0.00 0.00 0 95.76 0.00 0.00 0.02 0.36 1.55 2.31
206.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1665539 1665539 31.90 3.39 69.80 0.04 56.00 101 1665539 0.00 0.00 0 96.36 0.00 0.00 0.01 0.20 0.56 2.87
207.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2019222 2019222 31.80 2.08 65.81 0.46 54.00 101 2000000 0.00 0.00 0 95.07 0.00 0.00 0.00 0.28 1.64 3.01
208.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2486262 2486262 31.70 3.54 68.02 0.29 55.00 101 2000000 0.00 0.00 0 94.89 0.00 0.00 0.00 0.29 0.91 3.91
209.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2290328 2290328 31.90 4.83 64.94 0.13 56.00 101 2000000 0.00 0.00 0 94.76 0.00 0.00 0.00 0.08 0.55 4.61
210.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1932054 1932054 31.80 1.55 65.54 0.48 53.00 101 1932054 0.00 0.00 0 95.98 0.00 0.00 0.00 0.39 1.30 2.33
211.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1763329 1763329 31.70 3.91 69.89 0.08 55.00 101 1763329 0.00 0.00 0 95.42 0.01 0.00 0.00 0.23 0.69 3.65
212.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2578355 2578355 31.80 3.50 67.12 0.11 55.00 101 2000000 0.00 0.00 0 96.02 0.00 0.00 0.00 0.13 0.72 3.13
213.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1931628 1931628 31.80 3.16 68.28 0.15 55.00 101 1931628 0.00 0.00 0 96.02 0.00 0.01 0.00 0.29 0.80 2.88
214.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1871676 1871676 31.50 1.82 68.47 0.25 54.00 101 1871676 0.00 0.00 0 95.27 0.00 0.00 0.00 0.38 1.51 2.84
215.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 858707 858707 31.90 2.14 81.24 0.01 55.00 101 858707 0.00 0.00 0 97.62 0.00 0.00 0.00 0.51 0.17 1.70
216.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2236397 2236397 31.70 3.74 67.28 0.08 55.00 101 2000000 0.00 0.00 0 95.41 0.00 0.00 0.00 0.56 0.16 3.87
217.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1562347 1562347 31.80 3.34 70.35 0.15 55.00 101 1562347 0.00 0.00 0 96.04 0.00 0.00 0.00 0.24 0.81 2.91
218.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1340149 1340149 31.90 3.10 73.77 0.05 55.00 101 1340149 0.00 0.00 0 96.64 0.00 0.00 0.00 0.58 0.22 2.56
219.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2440976 2440976 31.60 4.79 66.73 0.07 56.00 101 2000000 0.00 0.00 0 94.74 0.00 0.00 0.00 0.20 0.62 4.44
220.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1343165 1343165 31.50 0.95 69.53 0.38 53.00 101 1343165 0.00 0.00 0 95.66 0.00 0.00 0.00 0.48 3.14 0.72
221.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1882131 1882131 31.90 3.51 67.99 0.05 55.00 101 1882131 0.00 0.00 0 96.18 0.00 0.00 0.00 0.51 0.18 3.13
222.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1971368 1971368 31.70 3.81 68.49 0.18 55.00 101 1971368 0.00 0.00 0 95.47 0.00 0.00 0.00 0.27 0.74 3.52
223.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2522576 2522576 31.80 7.00 62.95 0.11 57.00 101 2000000 0.00 0.00 0 92.54 0.00 0.00 0.00 0.53 0.24 6.69
224.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1993672 1993672 31.50 1.71 66.12 0.27 52.00 101 1993672 0.00 0.01 0 96.44 0.00 0.00 0.00 0.36 1.28 1.91
225.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1875136 1875136 31.80 4.30 67.53 0.13 55.00 101 1875136 0.00 0.00 0 95.59 0.00 0.00 0.00 0.19 0.70 3.52
226.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1934505 1934505 31.70 2.67 68.03 0.25 53.00 101 1934505 0.00 0.00 0 96.04 0.00 0.00 0.00 0.34 1.08 2.54
227.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2329194 2329194 31.80 4.49 67.22 0.14 55.00 101 2000000 0.00 0.00 0 94.85 0.00 0.00 0.00 0.20 0.64 4.31
228.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2865679 2865679 31.80 2.28 67.55 0.18 53.00 101 2000000 0.00 0.00 0 96.47 0.00 0.00 0.00 0.23 0.89 2.41
229.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2455592 2455592 31.90 3.49 67.57 0.09 54.00 101 2000000 0.00 0.00 0 95.91 0.00 0.00 0.01 0.26 0.80 3.02
230.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2235345 2235345 31.70 2.90 66.35 0.26 54.00 101 2000000 0.00 0.00 0 95.88 0.00 0.00 0.00 0.21 1.03 2.88
231.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2784129 2784129 31.80 2.99 65.43 0.13 53.00 101 2000000 0.00 0.00 0 96.52 0.00 0.00 0.00 0.21 0.67 2.60
232.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2308006 2308006 31.70 1.63 66.87 0.27 52.00 101 2000000 0.00 0.00 0 96.86 0.00 0.00 0.00 0.35 1.03 1.76
233.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2172390 2172390 31.80 3.34 67.36 0.16 55.00 101 2000000 0.00 0.00 0 95.55 0.00 0.00 0.00 0.25 1.03 3.17
234.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2745231 2745231 31.90 4.43 66.04 0.13 55.00 101 2000000 0.00 0.00 0 95.64 0.00 0.00 0.00 0.22 0.69 3.45
235.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2505639 2505639 31.60 2.85 68.36 0.18 54.00 101 2000000 0.00 0.00 0 95.86 0.00 0.00 0.00 0.28 1.06 2.80
236.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2611713 2611713 31.90 2.12 65.20 0.05 54.00 101 2000000 0.00 0.00 0 96.79 0.00 0.00 0.00 0.19 1.06 1.96
237.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2235168 2235168 31.80 2.57 65.26 0.16 53.00 101 2000000 0.00 0.00 0 96.13 0.00 0.00 0.00 0.31 1.06 2.50
238.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 1843389 1843389 31.50 2.45 71.00 0.06 54.00 101 1843389 0.00 0.00 0 96.52 0.00 0.00 0.00 0.31 0.82 2.35
239.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 3015433 3015433 31.90 3.46 66.17 0.10 55.00 101 2000000 0.00 0.00 0 96.06 0.00 0.00 0.00 0.19 0.85 2.90
24.2nd.seq.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2704908 2704908 31.90 5.13 64.26 0.08 56.00 101 2000000 0.00 0.00 0 94.23 0.00 0.00 0.00 0.53 0.20 5.04
40.2nd.seq.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2816261 2816261 31.90 5.02 64.10 0.12 57.00 101 2000000 0.00 0.00 0 93.85 0.00 0.00 0.00 0.26 0.82 5.07
8.2nd.seq.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2818477 2818477 31.70 3.87 67.88 0.15 55.00 101 2000000 0.00 0.00 0 94.80 0.00 0.00 0.00 0.32 0.98 3.90
98.2nd.seq.L001 Reddy2_Project_002 101 230411_VH00601_152_AACLJHTM5 2239425 2239425 31.90 3.66 67.32 0.06 55.00 101 2000000 0.00 0.00 0 95.84 0.00 0.00 0.00 0.70 0.19 3.27
Mean undef 101 230411_VH00601_152_AACLJHTM5 2468407 2468407 31.76 4.08 65.06 0.18 55.92 101 1872654 0.00 0.00 0 94.93 0.00 0.00 0.04 0.44 0.81 3.78


Order samples by

Reads per Sample

The number of reads per sample at the start of the analysis is shown.

Quality Summary

This plot shows the mean base quality score for each position in a fastq file. The higher the score the better the base call. Green indicates very good quality, yellow indicates reasonable quality, and red indicates poor quality. The quality of calls degrade as the sequencing run progresses, so it is common to see base calls turning yellow towards the end of a read. It is common to see base calls turning red in short insert libraries (16s/18s, small RNA, amplicon). This metric is calculated by FastQC.

Adapter Content

This plot shows the cumulative proportion of each sample in which sequencing adapter sequences have been seen at each position. Once an adapter sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages only increase as the read length goes on. It is common to see significant adapter sequence content at the ends of reads in short insert libraries (16s/18s, small RNA, amplicon). This metric is calculated by FastQC.

Library Diversity

This plot shows the percentage of reads that remain after deduplication (removing duplicated sequences), which is a measure of library diversity. Sequence data from genomic DNA libraries typically have high library diversity, and data from targeted sequencing libraries typically have low diversity. This metric is calculated by FastQC.

Sequence Content

The first 10,000 R1 reads from each sample are aligned to a selection of common reference genomes and sequence contaminants, and the number of reads aligning to each reference is shown. Reads aligning to multiple references are assigned to the reference with the most alignments. This plot provides a simple method to verify the sequence content of each library.